The variation in basal spacing distance in the Na-MMT/amine-containing drugs models during 1 ns molecular dynamics simulations.

George Tzotzos (5052083)
Jim N. Iley (5052086)
Elaine A. Moore (5052080)

April 2018

Distance between the centre of mass of the ligand and that of residues lying within 0.30 nm at th...

Chih-Chieh Chen (20257)
Tze-Kiong Er (378226)
Yen-Yi Liu (183718)
Jenn-Kang Hwang (20258)
Maria Jesus Barrio (378227)
Maximiliano Rodrigo (378228)
Enrique Garcia-Toro (378229)
Marta Herreros-Villanueva (105977)

February 2013

The molecular dynamics trajectories for: (A) Comparison of the RMSD plots of the sensitive sites ...

(A) Change in distance between the dyad and flap region in the 2B8L (purple) and 2FDP (green) systems in the respective cMD simulations.

M. Olivia Kim (818902)
Patrick G. Blachly (499863)
J. Andrew McCammon (12411)

October 2015

(B) Interactions between the bound inhibitor in the 2B8L complex and surrounding residues.</p

Drug-loaded amount, and experimental and simulate basal spacing of Na-MMT/amine-containing drugs complexes.

Murilo L. Bello (710437)
Aridio M. Junior (710438)
Bárbara A. Vieira (710439)
Luiza R. S. Dias (710440)
Valéria P. de Sousa (710441)
Helena C. Castro (710442)
Carlos R. Rodrigues (8332)
Lucio M. Cabral (710443)

March 2015

*No intercalation evident.**Basal spacing results of the models closer to experimental res...

Snapshots at 1ns of the molecular dynamics simulation of the Na-MMT/drugs models showing the basal spacing.

Murilo L. Bello (710437)
Aridio M. Junior (710438)
Bárbara A. Vieira (710439)
Luiza R. S. Dias (710440)
Valéria P. de Sousa (710441)
Helena C. Castro (710442)
Carlos R. Rodrigues (8332)
Lucio M. Cabral (710443)

March 2015

Structures in gray represent the periodic boundary conditions. The projection view is shown along...

Amine-containing drugs molecular properties and experimental observations.

Murilo L. Bello (710437)
Aridio M. Junior (710438)
Bárbara A. Vieira (710439)
Luiza R. S. Dias (710440)
Valéria P. de Sousa (710441)
Helena C. Castro (710442)
Carlos R. Rodrigues (8332)
Lucio M. Cabral (710443)

March 2015

(A) Comparison of the experimental and simulate basal spacing, and average interaction energies. ...

The distances between H11 and H12 of the four systems throughout the 100 ns molecular dynamics simulations.

Lanlan Li (181980)
Qianqian Wang (494839)
Yan Zhang (8098)
Yuzhen Niu (709953)
Xiaojun Yao (220558)
Huanxiang Liu (418534)

March 2015

The distances between H11 and H12 of the four systems throughout the 100 ns molecular dynamics si...

Configurations of lipids and NP ligands for different MUS ligand distributions.

Reid C. Van Lehn (1725733)
Alfredo Alexander-Katz (1511773)

January 2019

The top row presents representative simulation snapshots of the NP and lipid head groups for four MU...

Molecular dynamics simulations.

Chih-Wei Huang (572370)
Hui-Chen Lin (541723)
Chi-Yuan Chou (837167)
Wei-Chuo Kao (843434)
Wei-Yuan Chou (843435)
Hwei-Jen Lee (415061)

January 2016

(A) The distances between the Cα of specific residues located at the interfaces along ...

Distance profile of the N-terminal residues between the two chains as a function of simulation time.

Soma Ghosh (173803)
Nagasuma Chandra (153529)
Saraswathi Vishveshwara (34348)

January 2016

N-terminal stability between the two dimeric systems (with and without metal ion) is quantified b...

Determinants of drug-target interactions at the single cell level - Fig 4

Vlad Elgart (6107933)
Jia-Ren Lin (6107936)
Joseph Loscalzo (31315)

January 2019

(a) Numerical simulation (time dependent external concentration uext(t)) of overall dye incorporatio...

Distance between center of mass (COM) of DNA and dendrimers as a function of time.

Valeria Márquez-Miranda (797333)
María Belén Camarada (797334)
Ingrid Araya-Durán (797335)
Ignacio Varas-Concha (797336)
Daniel Eduardo Almonacid (797337)
Fernando Danilo González-Nilo (797338)

September 2015

PAMAM-Arg shows a shorter distance to DNA towards the end of MD simulations.</p

Inter-subunit interaction distances during molecular dynamics simulations.

Lívia Marton (756117)
Gergely N. Nagy (756118)
Olivér Ozohanics (756119)
Anikó Lábas (756120)
Balázs Krámos (756121)
Julianna Oláh (555121)
Károly Vékey (122026)
Beáta G. Vértessy (24771)

June 2015

A) Variation of the atomic distance d(R/H681, CA - H679’, O) as a characteristic proximal inter-s...

Distances between the NBDs.

Karmen Condic-Jurkic (1580293)
Nandhitha Subramanian (1580290)
Alan E. Mark (535969)
Megan L. O’Mara (535968)

January 2018

(A-C) Distances measured between the centres of mass (COM) of the nucleotide binding domai...

Analysis of the distances between the center of mass of the two subunits during the simulation time.

Stephane Marchal (5651677)
Anna Marabotti (68229)
Maria Staiano (69104)
Antonio Varriale (297193)
Thomas Domaschke (297195)
Reinhard Lange (297196)
Sabato D’Auria (297197)

February 2013

Variation of the distances of the center of mass of the two subunits of bOBP during the time, for...

AgamOBP1-multiligand complexes.

George Tzotzos (5052083)
Jim N. Iley (5052086)
Elaine A. Moore (5052080)

April 2018

Distance between the centre of mass of the ligand and that of residues lying within 0.30 nm at th...

Figure 2

Chih-Chieh Chen (20257)
Tze-Kiong Er (378226)
Yen-Yi Liu (183718)
Jenn-Kang Hwang (20258)
Maria Jesus Barrio (378227)
Maximiliano Rodrigo (378228)
Enrique Garcia-Toro (378229)
Marta Herreros-Villanueva (105977)

February 2013

The molecular dynamics trajectories for: (A) Comparison of the RMSD plots of the sensitive sites ...

(A) Change in distance between the dyad and flap region in the 2B8L (purple) and 2FDP (green) systems in the respective cMD simulations.

M. Olivia Kim (818902)
Patrick G. Blachly (499863)
J. Andrew McCammon (12411)

October 2015

(B) Interactions between the bound inhibitor in the 2B8L complex and surrounding residues.</p

Drug-loaded amount, and experimental and simulate basal spacing of Na-MMT/amine-containing drugs complexes.

Murilo L. Bello (710437)
Aridio M. Junior (710438)
Bárbara A. Vieira (710439)
Luiza R. S. Dias (710440)
Valéria P. de Sousa (710441)
Helena C. Castro (710442)
Carlos R. Rodrigues (8332)
Lucio M. Cabral (710443)

March 2015

*No intercalation evident.**Basal spacing results of the models closer to experimental res...

Snapshots at 1ns of the molecular dynamics simulation of the Na-MMT/drugs models showing the basal spacing.

Murilo L. Bello (710437)
Aridio M. Junior (710438)
Bárbara A. Vieira (710439)
Luiza R. S. Dias (710440)
Valéria P. de Sousa (710441)
Helena C. Castro (710442)
Carlos R. Rodrigues (8332)
Lucio M. Cabral (710443)

March 2015

Structures in gray represent the periodic boundary conditions. The projection view is shown along...

Amine-containing drugs molecular properties and experimental observations.

Murilo L. Bello (710437)
Aridio M. Junior (710438)
Bárbara A. Vieira (710439)
Luiza R. S. Dias (710440)
Valéria P. de Sousa (710441)
Helena C. Castro (710442)
Carlos R. Rodrigues (8332)
Lucio M. Cabral (710443)

March 2015

(A) Comparison of the experimental and simulate basal spacing, and average interaction energies. ...

The distances between H11 and H12 of the four systems throughout the 100 ns molecular dynamics simulations.

Lanlan Li (181980)
Qianqian Wang (494839)
Yan Zhang (8098)
Yuzhen Niu (709953)
Xiaojun Yao (220558)
Huanxiang Liu (418534)

March 2015

The distances between H11 and H12 of the four systems throughout the 100 ns molecular dynamics si...

Configurations of lipids and NP ligands for different MUS ligand distributions.

Reid C. Van Lehn (1725733)
Alfredo Alexander-Katz (1511773)

January 2019

The top row presents representative simulation snapshots of the NP and lipid head groups for four MU...

Molecular dynamics simulations.

Chih-Wei Huang (572370)
Hui-Chen Lin (541723)
Chi-Yuan Chou (837167)
Wei-Chuo Kao (843434)
Wei-Yuan Chou (843435)
Hwei-Jen Lee (415061)

January 2016

(A) The distances between the Cα of specific residues located at the interfaces along ...

Distance profile of the N-terminal residues between the two chains as a function of simulation time.

Soma Ghosh (173803)
Nagasuma Chandra (153529)
Saraswathi Vishveshwara (34348)

January 2016

N-terminal stability between the two dimeric systems (with and without metal ion) is quantified b...

Determinants of drug-target interactions at the single cell level - Fig 4

Vlad Elgart (6107933)
Jia-Ren Lin (6107936)
Joseph Loscalzo (31315)

January 2019

(a) Numerical simulation (time dependent external concentration uext(t)) of overall dye incorporatio...

Distance between center of mass (COM) of DNA and dendrimers as a function of time.

Valeria Márquez-Miranda (797333)
María Belén Camarada (797334)
Ingrid Araya-Durán (797335)
Ignacio Varas-Concha (797336)
Daniel Eduardo Almonacid (797337)
Fernando Danilo González-Nilo (797338)

September 2015

PAMAM-Arg shows a shorter distance to DNA towards the end of MD simulations.</p

Inter-subunit interaction distances during molecular dynamics simulations.

Lívia Marton (756117)
Gergely N. Nagy (756118)
Olivér Ozohanics (756119)
Anikó Lábas (756120)
Balázs Krámos (756121)
Julianna Oláh (555121)
Károly Vékey (122026)
Beáta G. Vértessy (24771)

June 2015

A) Variation of the atomic distance d(R/H681, CA - H679’, O) as a characteristic proximal inter-s...

Distances between the NBDs.

Karmen Condic-Jurkic (1580293)
Nandhitha Subramanian (1580290)
Alan E. Mark (535969)
Megan L. O’Mara (535968)

January 2018

(A-C) Distances measured between the centres of mass (COM) of the nucleotide binding domai...

Analysis of the distances between the center of mass of the two subunits during the simulation time.

Stephane Marchal (5651677)
Anna Marabotti (68229)
Maria Staiano (69104)
Antonio Varriale (297193)
Thomas Domaschke (297195)
Reinhard Lange (297196)
Sabato D’Auria (297197)

February 2013

Variation of the distances of the center of mass of the two subunits of bOBP during the time, for...

AgamOBP1-multiligand complexes.

George Tzotzos (5052083)
Jim N. Iley (5052086)
Elaine A. Moore (5052080)

April 2018

Distance between the centre of mass of the ligand and that of residues lying within 0.30 nm at th...

Figure 2

Chih-Chieh Chen (20257)
Tze-Kiong Er (378226)
Yen-Yi Liu (183718)
Jenn-Kang Hwang (20258)
Maria Jesus Barrio (378227)
Maximiliano Rodrigo (378228)
Enrique Garcia-Toro (378229)
Marta Herreros-Villanueva (105977)

February 2013

The molecular dynamics trajectories for: (A) Comparison of the RMSD plots of the sensitive sites ...

(A) Change in distance between the dyad and flap region in the 2B8L (purple) and 2FDP (green) systems in the respective cMD simulations.

M. Olivia Kim (818902)
Patrick G. Blachly (499863)
J. Andrew McCammon (12411)

October 2015

(B) Interactions between the bound inhibitor in the 2B8L complex and surrounding residues.</p

The variation in basal spacing distance in the Na-MMT/amine-containing drugs models during 1 ns molecular dynamics simulations.

Abstract

Extracted data

The variation in basal spacing distance in the Na-MMT/amine-containing drugs models during 1 ns molecular dynamics simulations.

Abstract

Extracted data

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